Output from the Identify QIAseq Multimodal DNA Library Kit Variants workflows
The following outputs are generated:
- Genome Browser View (
): A collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser as described in https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Track_lists.html.
- A Sample report (
) that contains compiled QC metrics from other reports and provides an overview of a given sample. The sample report also reports whether the QC thresholds specified in the Create Sample Report wizard dialog have been met.
- Variants passing filters: The filtered variants.
- QC & Reports folder:
- QC report (
): Summarizes and visualizes various statistics of the input DNA reads.
See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Sequencing_Reads.html for details.
- Trimmed reads report (): Summarizes the performed trimming. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html for details.
- Mapping report (): Summarizes the performed read mapping.
See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Summary_mapping_report.html for details.
- Remove ligation artifact report (): Summarizes ligation artifacts found in and removed from the read mapping. See Remove Ligation Artifacts for details.
- Coverage report (): Summarizes the coverage.
- For the hybrid capture workflows, the coverage is summarized within the target regions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Coverage_summary_report.html for details.
- For the WGS workflows, the coverage is summarized across the entire genome. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Read_Mapping.html for details.
- QC report (
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- UMI group report (): Summarizes the identified UMI groups.
See Calculate Unique Molecular Index Groups for details.
- UMI reads report (): Summarizes the UMI reads.
See Create UMI Reads from Grouped Reads for details.
Additionally, for the hybrid capture workflows:
- Structural variants report (): Summarizes the number and different types of identified structural variants. See Output from the Structural Variant Caller for details.
- CNV results report (): Summarizes the identified CNVs. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=CNV_results_report.html for details.
Additionally, for the workflow with TMB and MSI:
- MSI report (): Summarizes the performed MSI detection and contains the MSI status of the sample. See Output from Detect MSI Status for details.
- TMB report (): Contains the TMB score and confidence values. See Calculate TMB Score for details.
- Structural variants report (
- Tracks folder:
- Read mapping: The reads mapped to the reference genome.
- Unfiltered variants: The variants identified before filtering.
- Indels indirect evidence: The filtered indels.
Additionally, for the hybrid capture workflows:
- Gene-level CNV: Genes affected by CNVs.
- Region-level CNV: Regions affected by CNVs.
- Amino acid: Filtered variants annotated with amino acid changes.
- Per region statistics: Coverage statistics for each target region.
Additionally, for the workflow with TMB and MSI:
- Loci track: MSI loci annotated with predicted stability.
- TMB somatic variants: Filtered variants that were included in the TMB score calculation.